hicPCA¶

Computes PCA eigenvectors for a Hi-C matrix.

$ hicPCA –matrix hic_matrix.h5 -o pca1.bedgraph pca2.bedgraph

usage: hicPCA --matrix MATRIX --outputFileName OUTPUTFILENAME
              [OUTPUTFILENAME ...]
              [--numberOfEigenvectors NUMBEROFEIGENVECTORS]
              [--format {bedgraph,bigwig}]
              [--chromosomes CHROMOSOMES [CHROMOSOMES ...]] [--norm]
              [--geneTrack GENETRACK] [--pearsonMatrix PEARSONMATRIX]
              [--obsexpMatrix OBSEXPMATRIX] [--help] [--version]

Required arguments¶

–matrix, -m

HiCExplorer matrix in h5 format.

–outputFileName, -o

File names for the result of the pca. Number of output file must match the number of computed eigenvectors.

Default: [‘pca1’, ‘pca2’]

Optional arguments¶

`–numberOfEigenvectors, -noe`
	The number of eigenvectors that the PCA should compute. Default: 2
`–format, -f`	Possible choices: bedgraph, bigwig output format. Either bedgraph or bigwig. Default: “bigwig”
`–chromosomes`	List of chromosomes to be included in the correlation.
`–norm`	Different obs-exp normalization as used by Homer software. Default: False
`–geneTrack`	The gene track is needed to decide if the values of the eigenvector need a sign flip or not.
`–pearsonMatrix, -pm`
	Internally the input matrix is converted per chromosome to obs_exp matrix and consecutively to a Pearson matrix. Set this parameter to write the pearson matrix to a file.
`–obsexpMatrix, -oem`
	Internally the input matrix is converted per chromosome to obs_exp matrix and consecutively to a Pearson matrix. Set this parameter to write the observe / expected matrix to a file.
`–version`	show program’s version number and exit